We have conducted a comprehensive study of ground-state O(P-3) atomic oxygen reactions with 1-hexadecanethiolate (CH3(CH2)(10)SH) and 1-undecanethiolate (CH3(CH2)(10)SH) self-assembled monolayers adsorbed onto Au/mica substrates, using X-ray photoelectron spectroscopy, infrared reflection absorption spectroscopy, ellipsometry, and contact angle measurements. In general, the reactions are not limited to the terminal methyl groups. Apparently, the incident O(P-3) (translational energy per atom of 0.11 kJ mol(-1)) can penetrate below the surface of the monolayer. The ability of the atoms to penetrate, and thus the reaction rate of the backbone -CH2-, is dependent upon both the temperature and the chain length, with the longer chain having a large difference between the rate at room temperature and 150 K. In particular, the long-chain SAM exhibits clearly reduced reactivity with respect to the incident beam of atomic oxygen when the film is cooled to 150 K as compared to room temperature. This is a notable finding and demonstrates the crucial importance that structural order and dynamical fluctuations, both of which depend on chain length and substrate temperature, have in determining the surface passivation and protection characteristics of SAM overlayers with respect to attack by energetic reagents.